NLRC3 NLR family CARD domain containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NLRC3provided by HGNC
Official Full Name: NLR family CARD domain containing 3provided by HGNC
Primary source: HGNC:HGNC:29889
See related: Ensembl:ENSG00000167984 MIM:615648; AllianceGenome:HGNC:29889
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NOD3; CLR16.2
Summary: This gene encodes a NOD-like receptor family member. The encoded protein is a cytosolic regulator of innate immunity. This protein directly interacts with stimulator of interferon genes (STING), to prevent its proper trafficking, resulting in disruption of STING-dependent activation of the innate immune response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
Expression: Broad expression in lymph node (RPKM 6.9), spleen (RPKM 4.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (3539033..3577403, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (3566292..3604671, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (3589033..3627404, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Decoding the IBD paradox: A triadic interplay between REG3, enterococci, and NOD2.
Title: Decoding the IBD paradox: A triadic interplay between REG3, enterococci, and NOD2.
NLRC3 deficiency promotes hypoxia-induced pulmonary hypertension development via IKK/NF-kappaB p65/HIF-1alpha pathway.
Title: NLRC3 deficiency promotes hypoxia-induced pulmonary hypertension development via IKK/NF-κB p65/HIF-1α pathway.
NLRC3 is a potential prognostic biomarker that is correlated with immune cell infiltration in lung adenocarcinoma.
Title: NLRC3 is a potential prognostic biomarker that is correlated with immune cell infiltration in lung adenocarcinoma.
[Knockdown of NLRC3 promotes proliferation and invasion of human colon cancer cells].
Title: [Knockdown of NLRC3 promotes proliferation and invasion of human colon cancer cells].
NLRC3 silencing accelerates the invasion of hepatocellular carcinoma cell via IL-6/JAK2/STAT3 pathway activation.
Title: NLRC3 silencing accelerates the invasion of hepatocellular carcinoma cell via IL-6/JAK2/STAT3 pathway activation.
Down-regulated expression of NLRC3 may play an important role in cancer progression and prognosis of HCC by acting as a tumor suppressor.
Title: The correlation of NLRC3 expression with the progression and prognosis of hepatocellular carcinoma.
expression of NLRC3 was significantly associated with CD8+ T cells infiltration
Title: [Association of NLRC3 with prognosis and tumor immunity in patients with stage III colorectal cancer].
NLRC3 promoted K48-linked polyubiquitination and degradation of interleukin-1 receptor-associated kinase 1 (IRAK1).
Title: NLRC3 promotes host resistance against Pseudomonas aeruginosa-induced keratitis by promoting the degradation of IRAK1.
The NLRC3 interferes with the assembly and activity of the NALP3 inflammasome complex by competing with ASC for pro-caspase-1 binding.
Title: NLRC3 protein inhibits inflammation by disrupting NALP3 inflammasome assembly via competition with the adaptor protein ASC for pro-caspase-1 binding.
The extent of NLRC3 and AIM2 gene reduction was correlated with cancer progression.
Title: Expression profile of innate immune receptors, NLRs and AIM2, in human colorectal cancer: correlation with cancer stages and inflammasome components.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of NLR family, CARD domain containing 3 (NLRC3) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-60735 (e-PCR)
- UniSTS:9728

D8S2279 (e-PCR)
- UniSTS:473907

D17S610 (e-PCR)
- UniSTS:46230

MARC_17089-17090:1023823752:1 (e-PCR)
- UniSTS:268215

SHGC-61133 (e-PCR)
- UniSTS:15561

D16S3380 (e-PCR)
- UniSTS:474313

GDB:631813 (e-PCR)
- UniSTS:158430

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol 3-kinase regulatory subunit binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in T cell activation	IEP Inferred from Expression Pattern more info	PubMed
involved_in canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of NF-kappaB transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of NLRP3 inflammasome complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cytokine production involved in inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of epithelial cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of fibroblast proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of inflammatory response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interferon-alpha production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interferon-beta production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-6 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of non-canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of tumor necrosis factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in centriolar satellite	IDA Inferred from Direct Assay more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: NLR family CARD domain-containing protein 3

Names: CARD15-like protein; NACHT, LRR and CARD domains-containing protein 3; NOD-like receptor C3; caterpiller protein 16.2; nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033123.1 RefSeqGene

Range

4989..43359

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_178844.4 → NP_849172.2 NLR family CARD domain-containing protein 3

See identical proteins and their annotated locations for NP_849172.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the protein.

Source sequence(s)

AK090431, AK090476, AW271824, AY601811, BC027864, FJ889357

Consensus CDS

CCDS73817.1

UniProtKB/Swiss-Prot

Q5EY36, Q7RTR2, Q8NF48, Q8NI01, Q8NI02, Q8TEL3

UniProtKB/TrEMBL

C3VPR7

Related

ENSP00000352039.6, ENST00000359128.10

Conserved Domains (4) summary

cd00116
Location:766 → 1053

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:808 → 833

LRR_RI; leucine-rich repeat [structural motif]

pfam05729
Location:139 → 305

NACHT; NACHT domain

pfam13855
Location:974 → 1042

LRR_8; Leucine rich repeat

RNA

NR_075083.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in a 5' exon and contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK090431, AK090476, AW271824, AY601811, BC027864, FJ889357

Related

ENST00000615877.4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

3539033..3577403 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047433769.1 → XP_047289725.1 NLR family CARD domain-containing protein 3 isoform X1

UniProtKB/Swiss-Prot

Q5EY36, Q7RTR2, Q8NF48, Q8NI01, Q8NI02, Q8TEL3

UniProtKB/TrEMBL

C3VPR7
XM_047433770.1 → XP_047289726.1 NLR family CARD domain-containing protein 3 isoform X2
XM_047433771.1 → XP_047289727.1 NLR family CARD domain-containing protein 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

3566292..3604671 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379802.1 → XP_054235777.1 NLR family CARD domain-containing protein 3 isoform X1

UniProtKB/Swiss-Prot

Q5EY36, Q7RTR2, Q8NF48, Q8NI01, Q8NI02, Q8TEL3

UniProtKB/TrEMBL

C3VPR7
XM_054379803.1 → XP_054235778.1 NLR family CARD domain-containing protein 3 isoform X2
XM_054379804.1 → XP_054235779.1 NLR family CARD domain-containing protein 3 isoform X3